I am traveling for business....so I missed the start of my window install. my wife sent me some pictures today I am concern about the overall sealing and installation. The first two windows were install in brick.

These were screwed in the sides, gaps filled with foam and flashed in aluminum and caulked.

We originally requested all the windows that were in siding to have nail flanges as we were having new siding installed after the windows. yesterday the installer recommended not using the nail flanges (he was concerned about the depth of window and he thought that that screwing the side were more secure than the nail flanges).

They did 4 windows today and my wife questioned on how the sealing tape would be applied (the installer stated that the tape is only used on installs with the nail flanges, and with this install foam is all that is needed).

So I think all they did was remove the old window, shimmed the new window, screwed it in and applied foam sealer.

I am concerned about this can you guys give some feedback on the install pictures (I will attach some below)

Without knowing more about the siding, it tough to render any feedback on the install.

A flange is ideal and where I will choose to disagree with your installer is in his statement that screwing through the jambs is more secure. The nailing flange, if an option, provides a very good attachment to the structure and as you noted, the ability to cover the flashing tape and create a continuous drainage/moisture barrier.

That being said, doing the window in an insert capacity does not mean that it is going to leak if it is done properly.

So far this is as far as the install has gone....no siding or flashing has been installed beyond what you see in the pictures... they have only done the 2nd floor windows.

The installer was more comfortable using this installation method ( and stated there was really no difference between this and the nail flange).

We are very concerned about proper sealing of the windows to the siding as we plan to be in this house for a long time. When he recommended to go the insert style as you suggest he never mention that the window would not be taped with that black membrane tape.

I guess I was thinking even if he installed them in the insert method the bottom of the rough opening should have been sealed with the tape (in the event that this window it self would leak). I feel that the foam in the pictures is only really for insulation and if the window did leak it would keep water in (as opposed to getting out on top of the tyvek).

At this point I am not sure how to proceed/remedy the situation.... can the upstairs windows be removed now that they have been Foamed in? Or will this just cause more issues? The first floor windows due to there location are subject to a lot more weather.

Who was the salesman?
What does your contract state about the install?
Did the windows come with fins on them.
Who is doing the siding work? Who is doing the capping in the non siding(brick) areas?
Who and with what is the inside being finished?

Andy, if everything is done properly, you don't have anything to worry about. Your installer is basically installing the windows in the same method that replacement (not new construction) windows are installed on a regular basis. That foam should be closed cell so it will seal against air and moisture, and the last details that will determine the quality of the install will be how the opening is flashed in order to shed water away and out.
That said, you SHOULD get what you paid for, so you may have a bone to pick if you were promised a nailing flange and flashing tape. That type of install is a little bit more labor intensive and does offer some added protection, so if it was specified on your contract it would not be out of line to request a partial refund, or to have the windows installed the way that they were spec'd out.
If your installer found something to make change the type of install, for instance that the offset of the nailing flange would cause problems with setting the window at the proper depth (alleviating the need for new jamb extensions, etc)- that could be a legit issue, but that should have been thoroughly explained and "ok'd" by you prior to going through with it.

Sounds like some communication issues between you and your installer or he changed things without telling you? I would not pay him if you were told or hopefully stated in the contract that you would get full frames. You may want check the details of siding bid as well why you are at it. Nail fins/full frame are a superior and more involved install but not always the best option.